Thank you Sarah for sharing about this!

Since I am the author of this plugin, I can say that you did a great job figuring what I wanted to do!

To answer you question, there are mainly two reasons that explain why I chose to wrap the URL in an embed shortcode. First, it allows to insert multiple embeds at once using the media manager selection toolbar. Second, it also gives the flexibility to add different options like autoplay that could be set directly from the media manager attachement details tab in future releases.

I have plenty of improvements under way, starting with a new release coming this week including basic flickr support. Also, people might want to check out for the upcoming release of premium add-ons that will allow more advanced feature like direct upload, syncing and updating your remote medias details here: http://onecodeshop.com/remote-media-library-pro/

I pay close attention to comments and suggestions, so keep them coming!